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Background  Previously rare  A2ML1  variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children. The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an  A2ML1  duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access.    Methods  Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media, of whom 11 carry the  A2ML1  duplication variant. Ear swabs were submitted for 16S rRNA gene sequencing.    Results  Genotype-based differences in microbial richness, structure, and composition were identified, but were not statistically significant. Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes, and genus  Fusobacterium  were nominally increased in carriers compared to non-carriers, but were non-significant after correction for multiple testing. We also detected rare bacteria including  Oligella  that was reported only once in the middle ear.    Conclusions  These findings suggest that  A2ML1- related otitis media susceptibility may be mediated by changes in the middle ear microbiome. Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community.    Electronic supplementary material  The online version of this article (doi:10.1186/s40249-016-0189-7) contains supplementary material, which is available to authorized users.

Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene